Exlude secondary source elements by matching rather than substraction (…

…asciidoctor#410)

This is a very subtle issue. When two Filtree instances are subtracted from each other
in order to eliminate a set of files, the base directory of the tree is lost. If this is
in a CopySpec the relative paths will thus also be lost. The solution is to use a matcher
of type PatternFilterable and then to exclude by FileTreeElement.

When using

asciidoctor-gradle-base/src/main/groovy/org/asciidoctor/gradle/base/AbstractAsciidoctorBaseTask.groovy

@@ -28,7 +28,9 @@ import org.gradle.api.InvalidUserDataException
 import org.gradle.api.artifacts.Configuration
 import org.gradle.api.file.CopySpec
 import org.gradle.api.file.FileTree
+import org.gradle.api.file.FileTreeElement
 import org.gradle.api.provider.Provider
+import org.gradle.api.specs.Spec
 import org.gradle.api.tasks.Console
 import org.gradle.api.tasks.Input
 import org.gradle.api.tasks.InputFiles
@@ -38,6 +40,7 @@ import org.gradle.api.tasks.OutputDirectories
 import org.gradle.api.tasks.OutputDirectory
 import org.gradle.api.tasks.PathSensitive
 import org.gradle.api.tasks.SkipWhenEmpty
+import org.gradle.api.tasks.util.PatternFilterable
 import org.gradle.api.tasks.util.PatternSet
 import org.ysb33r.grolifant.api.FileUtils
 import org.ysb33r.grolifant.api.StringUtils
@@ -672,9 +675,14 @@ abstract class AbstractAsciidoctorBaseTask extends DefaultTask {
      * @return Source tree based upon configured pattern.
      */
     protected FileTree getSecondarySourceFileTreeFrom(File dir) {
-        FileTree initialTree = project.fileTree(dir).
-            matching(this.secondarySourceDocumentPattern ?: defaultSecondarySourceDocumentPattern)
-        (initialTree - getSourceFileTreeFrom(dir)).asFileTree
+        FileTree doNotInclude = getSourceFileTreeFrom(dir)
+        project.fileTree(dir)
+            .matching(this.secondarySourceDocumentPattern ?: defaultSecondarySourceDocumentPattern)
+            .matching { PatternFilterable target ->
+                target.exclude({ FileTreeElement element ->
+                    doNotInclude.contains(element.file)
+                } as Spec<FileTreeElement>)
+            }
     }
 
     /** The default PatternSet that will be used if {@code sources} was never called

asciidoctor-gradle-jvm-epub/src/main/groovy/org/asciidoctor/gradle/jvm/epub/AsciidoctorEpubTask.groovy

@@ -60,7 +60,7 @@ class AsciidoctorEpubTask extends AbstractAsciidoctorTask {
         kindleGenExtension = project.extensions.getByType(KindleGenExtension)
         sourceDir = 'src/docs/asciidocEpub'
 
-        // TODO: We are setting this curretnly to fix a problem in asciidoctor-epub GEM.
+        // TODO: We are setting this currently to fix a problem in asciidoctor-epub GEM.
         useIntermediateWorkDir()
     }